Computer and Information SciencesBlogger
Rants, raves (and occasionally considered opinions) on phyloinformatics, taxonomy, and biodiversity informatics. For more ranty and less considered opinions, see my Twitter feed.
ISSN 2051-8188. Written content on this site is licensed under a Creative Commons Attribution 4.0 International license.

The problem with GBIF's Phylogeny Explorer


GBIF recently released the Phylogeny Explorer, using legumes as an example dataset. The goal is to enables users to “view occurrence data from the GBIF network aligned to legume phylogeny.” The screenshot below shows the legume phylogeny side-by-side with GBIF data.

Sub-second searching of millions of DNA barcodes using a vector database


Recently I’ve been messing about with DNA barcodes. I’m junior author with David Schindel on forthcoming book chapter Creating Virtuous Cycles for DNA Barcoding: A Case Study in Science Innovation, Entrepreneurship, and Diplomacy, and I’ve blogged about Adventures in machine learning: iNaturalist, DNA barcodes, and Lepidoptera. One thing I’ve always wanted is a simple way to explore DNA barcodes both geographically and phylogenetically.

What, if anything, is the Biodiversity Knowledge Hub?


To much fanfare BiCIKL launched the “Biodiversity Knowledge Hub” (see Biodiversity Knowledge Hub is online!!!). This is advertised as a “game-changer in scientific research”. The snappy video in the launch tweet claims that the hub will it will help your research thanks to interlinked data… …and responds to complex queries with the services provided… Interlinked data, complex queries, this all sounds very impressive.

Adventures in machine learning: iNaturalist, DNA barcodes, and Lepidoptera


Recently I’ve been working with a masters student, Maja Nagler, on a project using machine learning to identify images of Lepidoptera. This has been something of an adventure as I am new to machine learning, and have only minimal experience with the Python programming language. So what could possibly go wrong?

A taxonomic search engine


Tony Rees commented on my recent post Ten years and a million links. I’ve responded to some of his comments, but I think the bigger question deserves more space, hence this blog post. Tony’s comment Hi Rod, I like what you’re doing.

ChatGPT, semantic search, and knowledge graphs


One thing about ChatGPT is it has opened my eyes to some concepts I was dimly aware of but am only now beginning to fully appreciate. ChatGPT enables you ask it questions, but the answers depend on what ChatGPT “knows”. As several people have noted, what would be even better is to be able to run ChatGPT on your own content. Indeed, ChatGPT itself now supports this using plugins.

ChatGPT, of course


I haven’t blogged for a while, work and other reasons have meant I’ve not had much time to think, and mostly I blog to help me think. ChatGPT is obviously a big thing at the moment, and once we get past the moral panic (“students can pass exams using AI!”) there are a lot of interesting possibilities to explore.